The manipulation of functional gene sequences is the basis of molecular cloning. Ready availability of synthetic genes at a reasonable cost will accelerate the transformation of gene sequence information into gene function information. Deliberately-designed and unique-sequence synthetic genes will provide a stimulus to gene expression studies by making mutant proteins more available for study.
The classic method of de novo gene synthesis entails sequential annealing (hybridization) and ligation of the component synthetic oligonucleotides, a few at a time, in a homogeneous aqueous solution (Khorana, 1979; Blackburn, 1996). In this method, a mixture of overlapping, complementary oligonucleotides are annealed under conditions that favor formation of a correct double-stranded fragment (duplex DNA) with strand interruptions (nicks) at adjacent positions along the two strands. The resultant construct is then isolated and submitted to subsequent rounds of annealing, ligation, and isolation. The method requires efficient, rapid, and specific hybridization, the chemical synthesis of all the components of the gene, and many analytical and purification operations.
Purification of the intermediate duplex fragments after annealing and ligation is often complicated and ineffective in removing all misaligned, truncated, and otherwise imperfect constructs. Additionally, optimum hybridization of all duplex fragments and oligonucleotides is dependent on expert selection of the oligonucleotides within the gene. While the resulting double-stranded polynucleotide can be prepared up to several kilobases in length, the yield is typically less than 1% and the synthetic gene constructs have severely diminished biological activity relative to native genes when measured by protein expression levels (Agarwal, 1970).
Limitations to the classic method of gene synthesis include the known imperfections in chemical oligonucleotide synthesis, especially long oligonucleotides, resulting in impurities resulting from (i) failed-to-couple, truncated sequences, (ii) nucleobase-modified sequences, (iii) incompletely deprotected sequences, and (iv) other nucleotidic and non-nucleotidic by-products. Hybridization of impure oligonucleotide mixtures can lead to mismatches and impaired hybridization and ligation efficiency. The net result is low yields of functional, correct sequence oligonucleotides for use in synthetic gene assembly. An efficient method for the rapid and economical assembly of polynucleotides, i.e. genes or gene fragments, is desirable.